Comment 17 for bug 204770

This bug is a consequence of a longstanding upstream bug:

http://bugzilla.gnome.org/show_bug.cgi?id=164786 (gdm frontend runs entirely as root)

Notice that this upstream bug was opened in 2005, currently shows an assigned status, a priority=high and a severity=major.

This bug has been the source of annoyances for ubuntu users for a long time as can be seen by
https://bugs.launchpad.net/ubuntu/+bug/27156

The reason it manifests itself in a more direct fashion now is due to tracker. The delay you are seeing is related with the indexing tracker does the first time it is run for a user.

ps aux | grep root shows gvfs and trackerd processes running as root, that started just after running gksu gdmsetup in my normal account.

ls -al /root/.config/tracker
ls -al /root/.local/share/tracker
ls -al /root/.gvfs

also confirms this.